Week 7 HW: Genetic Circuits Part II: Neuromorphic Circuits

Assignment Part 1: Intracellular Artificial Neural Networks (IANNs)

  1. What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions?

Integrated Artificial Neural Networks (IANNs) offer superior advantages over traditional Boolean genetic circuits by enabling analog processing, high-dimensional pattern recognition, and robust adaptability. Unlike Boolean circuits (on/off), IANNs handle continuous input levels, allowing complex decision-making, such as classifying disease states based on weighted molecular signatures rather than simple threshold switches.

Advantages of IANNs

  • They can handle more complex signals (not just ON/OFF).
  • They can combine many inputs at once.
  • They give graded responses (not just yes/no).
  1. Describe a useful application for an IANN; include a detailed description of input/output behavior, as well as any limitations an IANN might face to achieve your goal.

Use: Detect cancer cells inside the body

Inputs:

X1 = cancer marker 1

X2 = cancer marker 2

Output:

If both markers are high → produce drug (kill cell)

If not → do nothing

Limitations:

  • Hard to control inside real cells
  • Can be slow
  • May make mistakes (wrong output)
  1. Below is a diagram depicting an intracellular single-layer perceptron where the X1 input is DNA encoding for the Csy4 endoribonuclease and the X2 input is DNA encoding for a fluorescent protein output whose mRNA is regulated by Csy4. Tx: transcription; Tl: translation.

Assignment Part 2: Fungal Materials

  1. What are some examples of existing fungal materials and what are they used for? What are their advantages and disadvantages over traditional counterparts?

Examples

  • Mycelium packaging Used instead of plastic/foam

  • Mycelium leather Used for clothes, bags

  • Building materials Used for bricks/insulation

Advantages:

  1. Biodegradable
  2. Eco-friendly
  3. Renewable

Disadvantages:

  1. Not as strong as plastic/metal

  2. Can be damaged by water

  3. Slower to produce

  4. What might you want to genetically engineer fungi to do and why? What are the advantages of doing synthetic biology in fungi as opposed to bacteria?

What we could make fungi do:

  • Produce stronger materials
  • Glow (for lighting)
  • Clean pollution

Why fungi (vs bacteria):

  • Grow into solid shapes (good for materials)
  • Naturally make strong structures
  • Better for large-scale materials